Provisional LSP RNAseq data management and processing workflow

LSP_RNAseq_workflow.md

You will perform all of the steps below from the Unix system transfer.rc.hms.harvard.edu, which you access via SSH using your eCommons username and password. The examples below use the username abc123, so in the typed commands after the $ you must substitute your own username (or the username of whomever you're working on behalf of).

1. Download the primary sequence data to ImStor

abc123@transfer:~$ cd /n/files/ImStor/sorger/data/rnaseq
abc123@transfer:/n/files/ImStor/sorger/data/rnaseq$ mkdir abc123
abc123@transfer:/n/files/ImStor/sorger/data/rnaseq$ cd abc123
abc123@transfer:/n/files/ImStor/sorger/data/rnaseq/abc123$ mkdir project_name
abc123@transfer:/n/files/ImStor/sorger/data/rnaseq/abc123$ cd project_name

Now, follow the data download instructions from your sequencing facility.

2. Copy the sequence data to /n/scratch2

abc123@transfer:/n/files/ImStor/sorger/data/rnaseq/abc123/project_name$ cd ..
abc123@transfer:/n/files/ImStor/sorger/data/rnaseq/abc123$ mkdir /n/scratch2/abc123
abc123@transfer:/n/files/ImStor/sorger/data/rnaseq/abc123$ rsync -avP project_name /n/scratch2/abc123
abc123@transfer:/n/files/ImStor/sorger/data/rnaseq/abc123$ exit

It's important not to put a trailing / on project_name in the rsync command. (If you include the /, the files will end up one directory level too high)

I have a PC and don't ssh in - I used putty to log into transfer.rc.hms.harvard.edu

Thanks, I've updated the text to incorporate that.